Can you export stl file from one object in one layer?
When exporting from File > Export > STL in the file browser tool shelf, in the bottom right tick the option Selection Only.

This will export you current selection though, I don't think there is a direct way to export current layer only, but you can easily select all visible objects if you turn off other layers so it should suffice.

You may need to be in object mode for this to work though